Variant report

Variant	rs12203820
Chromosome Location	chr6:167363511-167363512
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr6:167362999-167364205	MCF-7	breast:	n/a	n/a
2	POLR2A	chr6:167363349-167365201	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:167363141-167365064	GM19193	blood:	n/a	n/a
4	POLR2A	chr6:167362972-167363518	HepG2	liver:	n/a	n/a
5	POLR2A	chr6:167363085-167364460	HepG2	liver:	n/a	n/a
6	NR2F2	chr6:167362984-167363881	MCF-7	breast:	n/a	n/a
7	POLR2A	chr6:167362977-167365124	GM12891	blood:	n/a	n/a
8	RUNX3	chr6:167363485-167364297	GM12878	blood:	n/a	n/a
9	ZNF217	chr6:167363090-167363788	MCF-7	breast:	n/a	n/a
10	POLR2A	chr6:167363089-167365108	GM12878	blood:	n/a	n/a
11	MTA3	chr6:167363331-167364435	GM12878	blood:	n/a	n/a
12	MAX	chr6:167363115-167364183	MCF-7	breast:	n/a	n/a
13	MTA3	chr6:167362913-167365179	GM12878	blood:	n/a	n/a
14	FOXA1	chr6:167363503-167363648	T-47D	breast:	n/a	n/a
15	RELA	chr6:167363485-167364409	GM18505	blood:	n/a	n/a
16	POLR2A	chr6:167363114-167365106	GM18505	blood:	n/a	n/a
17	SPI1	chr6:167363509-167364295	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:167363482-167363638	HepG2	liver:	n/a	n/a
19	TCF7L2	chr6:167363204-167363677	MCF-7	breast:	n/a	n/a
20	TBL1XR1	chr6:167363125-167365112	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:167363031-167365932	GM12878	blood:	n/a	n/a
22	STAT5A	chr6:167363479-167365181	GM12878	blood:	n/a	chr6:167363978-167363989
23	POLR2A	chr6:167363489-167365216	GM12878	blood:	n/a	n/a
24	GATA3	chr6:167363462-167364268	MCF-7	breast:	n/a	chr6:167363741-167363749
25	GATA3	chr6:167363316-167363908	MCF-7	breast:	n/a	chr6:167363741-167363749
26	BCLAF1	chr6:167363456-167364277	GM12878	blood:	n/a	chr6:167363938-167363947
27	RELA	chr6:167363204-167365104	GM15510	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:167361983..167365004-chr6:167367480..167371949,7	MCF-7	breast:
2	chr6:167358096..167360750-chr6:167361902..167364646,4	K562	blood:
3	chr6:167362668..167365438-chr6:167411450..167414365,2	MCF-7	breast:
4	chr6:167353412..167356832-chr6:167362421..167365420,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197146	TF binding region
ENSG00000272980	Chromatin interaction
ENSG00000249141	Chromatin interaction
ENSG00000213066	Chromatin interaction
ENSG00000026297	Chromatin interaction
ENSG00000227598	Chromatin interaction
ENSG00000197146	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10946197	1.00[ASN][1000 genomes]
rs12197030	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12199182	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12205779	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13220568	1.00[ASN][1000 genomes]
rs2236311	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55843050	1.00[ASN][1000 genomes]
rs62436419	1.00[ASN][1000 genomes]
rs62436761	1.00[ASN][1000 genomes]
rs62438869	1.00[ASN][1000 genomes]
rs71571466	1.00[ASN][1000 genomes]
rs9457237	1.00[ASN][1000 genomes]
rs9457243	1.00[ASN][1000 genomes]
rs9459809	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1019381	chr6:167090236-167558598	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv538541	chr6:167090236-167558598	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv948634	chr6:167200671-167838993	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
5	nsv482507	chr6:167282376-167474915	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv532074	chr6:167320656-167781977	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1031039	chr6:167324021-167741439	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
8	nsv538543	chr6:167324021-167741439	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
9	nsv1026972	chr6:167335031-167671042	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
10	nsv1034359	chr6:167359643-167384714	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167341000-167368800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr6:167341200-167368800	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:167342400-167368600	Weak transcription	Fetal Heart	heart
4	chr6:167344200-167364000	Weak transcription	Brain Angular Gyrus	brain
5	chr6:167344200-167368600	Weak transcription	Right Atrium	heart
6	chr6:167344400-167363600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:167344400-167364000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:167348400-167364800	Weak transcription	Brain Substantia Nigra	brain
9	chr6:167350000-167363600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr6:167350600-167366400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:167350600-167367600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr6:167352200-167368800	Weak transcription	Fetal Kidney	kidney
13	chr6:167352400-167364800	Weak transcription	Right Ventricle	heart
14	chr6:167353600-167364000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:167353800-167366600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:167354400-167364800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr6:167354600-167364800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:167354600-167368800	Weak transcription	HSMM	muscle
19	chr6:167354600-167369000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr6:167354600-167369000	Weak transcription	A549	lung
21	chr6:167356400-167366800	Strong transcription	Fetal Intestine Small	intestine
22	chr6:167357200-167364000	Weak transcription	Left Ventricle	heart
23	chr6:167359200-167365400	Strong transcription	Primary hematopoietic stem cells	blood
24	chr6:167360000-167368800	Weak transcription	Fetal Lung	lung
25	chr6:167360600-167368800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:167360600-167368800	Weak transcription	Fetal Muscle Leg	muscle
27	chr6:167360600-167369000	Weak transcription	Osteobl	bone
28	chr6:167361200-167363600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr6:167361200-167364800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr6:167361200-167366200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:167361200-167369000	Weak transcription	Ovary	ovary
32	chr6:167361200-167369200	Weak transcription	Aorta	Aorta
33	chr6:167361400-167363600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr6:167361400-167363800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:167361400-167363800	Weak transcription	Fetal Brain Female	brain
36	chr6:167361400-167364000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr6:167361400-167364000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr6:167361600-167363800	Weak transcription	Liver	Liver
39	chr6:167361600-167363800	Weak transcription	Fetal Intestine Large	intestine
40	chr6:167361800-167368600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr6:167361800-167369000	Weak transcription	Psoas Muscle	Psoas
42	chr6:167362200-167365800	Genic enhancers	HepG2	liver
43	chr6:167362200-167368800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:167362400-167363600	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr6:167362600-167365400	Enhancers	Placenta	Placenta
46	chr6:167362800-167363600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr6:167363000-167363800	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr6:167363000-167363800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
49	chr6:167363000-167364000	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr6:167363000-167364200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood

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